Paratuberculosis is a chronic infection of the intestine, mainly the ileum, caused by Mycobacterium avium subsp. paratuberculosis (Map) in ruminants. This enzootic disease is present worldwide and has a strong impact on the dairy cattle industry. For this species, the typing tools do not make it possible to track the spread and microevolution of the strains. These limitations can be overcome by the application of Whole Genome Sequencing (WGS), particularly for clonal populations such as Map. WGS analyses can provide comprehensive genetic information, including information on genome evolution and discrimination of closely related strains. The purpose of the present study was to undertake a whole-genome analysis of Map strains to identify accurate phylogenetic relationships between isolates and establish correlations between genomic traits and epidemiological data within a population of well documented-strains. A set of 200 animal field strains, representative of the French Map population circulating in the West of France, were isolated from bovine of breed Prim'Holstein or Normande naturally infected by Map. For each strain isolated, all information about the animal is available including: herd prevalence, locations, serological status and excretion level. Map strains were sequenced on an Illumina MiSeq. Genomic sequences were assessed for potential contamination. Reads were aligned to a local reference to infer a SNP-based phylogeny. This study provided 200 new genomes of French strain isolates from naturally infected animals. Pangenome analysis of this panel confirmed the degree of Map clonality. SNP analysis provided accurate phylogeny able to distinguish each strain divided into 3 clusters independently of the cattle’s breed. Interestingly, clusters seem associated with the two major MLVA profiles. A phylogeny was inferred with French Map isolates and with other Map isolates found across the world. Relationships between genetic traits and epidemiological data will be investigated to better understand the transmission dynamics of the disease.